BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 3 6 3 151.35 0.73 2 3 7 4 149.00 1.91 3 4 7 3 149.01 1.91 4 4 8 4 149.01 1.91 5 4 118 114 20.79 0.18 6 5 8 3 151.22 1.59 7 5 9 4 151.35 1.54 8 5 116 111 22.57 0.02 9 5 118 113 21.86 0.34 10 6 9 3 151.35 1.54 11 6 10 4 151.35 1.54 12 7 10 3 151.35 1.54 13 7 11 4 151.35 1.54 14 8 11 3 151.35 1.54 15 8 12 4 150.50 1.11 16 8 13 5 146.42 3.16 17 8 54 46 63.37 2.93 18 8 108 100 35.56 0.03 19 8 117 109 35.73 0.01 20 8 118 110 35.61 0.04 21 8 119 111 35.55 0.02 22 8 120 112 35.52 0.01 23 9 12 3 150.52 1.13 24 9 13 4 139.76 1.27 25 9 33 24 120.34 1.03 26 9 51 42 80.28 1.50 27 10 33 23 120.14 0.97 28 10 34 24 120.48 1.09 29 10 35 25 120.48 1.09 30 11 35 24 120.48 1.09 31 11 41 30 121.53 0.96 32 11 44 33 115.66 0.55 33 11 46 35 114.34 0.10 34 12 41 29 122.14 1.20 35 12 44 32 118.80 0.59 36 12 45 33 114.47 0.05 37 12 46 34 114.34 0.11 38 12 47 35 114.33 0.10 39 12 120 108 35.69 0.01 40 13 33 20 122.41 1.20 41 13 47 34 114.36 0.10 42 13 49 36 114.31 0.10 43 13 50 37 114.29 0.10 44 13 51 38 108.81 0.49 45 13 54 41 88.17 1.61 46 14 17 3 170.53 2.64 47 14 25 11 120.48 1.10 48 14 29 15 121.26 0.96 49 14 33 19 122.44 1.21 50 14 46 32 119.82 1.07 51 14 47 33 118.37 0.81 52 14 48 34 114.35 0.10 53 15 49 34 114.34 0.11 54 15 50 35 114.28 0.09 55 17 48 31 120.40 1.10 56 18 48 30 120.53 1.06 57 18 80 62 120.50 1.06 58 19 48 29 121.08 0.92 59 19 80 61 120.54 1.05 60 19 101 82 121.84 1.12 61 20 25 5 122.54 1.20 62 20 48 28 122.29 1.20 63 20 82 62 122.30 1.20 64 20 99 79 122.41 1.26 65 20 101 81 122.12 1.22 66 21 25 4 124.27 0.36 67 22 25 3 146.41 1.84 68 22 99 77 152.41 0.33 69 23 99 76 151.61 0.73 70 24 28 4 337.76 0.46 71 25 29 4 337.78 0.45 72 25 46 21 181.11 0.68 73 25 48 23 167.06 0.43 74 25 82 57 169.00 0.06 75 25 99 74 186.37 1.95 76 26 30 4 337.68 0.40 77 26 82 56 237.21 0.31 78 26 97 71 216.93 0.22 79 26 98 72 215.43 0.55 80 26 99 73 197.83 0.21 81 27 96 69 232.82 0.53 82 27 97 70 225.24 0.08 83 29 46 17 233.28 0.81 84 30 35 5 336.68 0.34 85 30 36 6 303.73 14.49 86 30 41 11 233.88 0.66 87 30 44 14 233.81 0.68 88 30 46 16 233.47 0.72 89 30 97 67 233.55 0.75 90 31 36 5 330.68 1.93 91 33 46 13 233.54 0.68 92 35 41 6 244.37 4.53 93 35 44 9 233.90 0.66 94 35 46 11 233.88 0.66 95 36 40 4 336.38 0.49 96 36 95 59 335.81 0.15 97 36 97 61 335.45 0.03 98 40 86 46 233.92 0.68 99 42 85 43 233.87 0.67 100 42 86 44 233.88 0.67 101 43 84 41 233.81 0.69 102 43 85 42 233.81 0.69 103 44 83 39 233.81 0.69 104 44 84 40 233.74 0.70 105 45 81 36 233.86 0.68 106 45 82 37 233.80 0.69 107 45 83 38 233.73 0.71 108 45 120 75 38.66 1.15 109 46 81 35 233.80 0.69 110 46 82 36 233.78 0.70 111 46 84 38 233.72 0.71 112 47 79 32 233.86 0.68 113 47 80 33 233.80 0.69 114 47 81 34 233.72 0.70 115 47 106 59 244.94 38.02 116 47 120 73 39.59 1.44 117 48 80 32 233.75 0.70 118 48 81 33 233.71 0.71 119 48 82 34 233.70 0.71 120 49 79 30 233.78 0.69 121 49 80 31 233.74 0.70 122 53 79 26 233.47 0.73 123 54 79 25 230.33 1.30 124 54 117 63 56.73 1.45 125 55 116 61 61.34 0.83 126 55 117 62 57.09 1.61 127 57 73 16 233.59 0.70 128 57 74 17 233.58 0.71 129 57 75 18 218.74 0.69 130 57 79 22 209.70 0.58 131 58 73 15 233.52 0.72 132 58 115 57 62.90 0.94 133 58 116 58 62.84 0.92 134 58 117 59 62.80 0.87 135 60 74 14 233.63 0.72 136 60 75 15 233.25 0.89 137 60 76 16 223.53 2.08 138 61 73 12 233.68 0.71 139 61 74 13 233.62 0.71 140 61 76 15 232.56 0.55 141 62 70 8 256.44 0.56 142 62 72 10 233.80 0.69 143 62 73 11 233.69 0.71 144 63 70 7 330.61 2.19 145 63 72 9 233.83 0.68 146 63 73 10 233.80 0.69 147 63 74 11 233.77 0.68 148 63 107 44 233.81 0.68 149 64 72 8 252.18 0.16 150 65 109 44 233.58 0.69 151 65 121 56 57.39 1.51 152 66 121 55 61.54 0.92 153 66 122 56 61.54 0.92 154 71 109 38 233.63 0.71 155 71 110 39 233.62 0.71 156 71 111 40 233.56 0.69 157 71 115 44 160.50 1.03 158 72 107 35 233.72 0.71 159 72 108 36 233.63 0.71 160 72 109 37 233.50 0.72 161 72 121 49 56.97 1.31 162 73 107 34 233.63 0.72 163 73 108 35 233.59 0.73 164 73 110 37 232.75 0.42 165 73 115 42 134.30 3.33 166 74 105 31 233.75 0.70 167 74 106 32 233.63 0.72 168 74 107 33 232.91 0.51 169 74 124 50 41.10 1.11 170 75 79 4 215.34 0.52 171 75 105 30 233.64 0.72 172 75 106 31 233.59 0.72 173 76 105 29 233.62 0.72 174 77 105 28 232.78 0.43 175 78 103 25 233.59 0.73 176 78 104 26 217.34 0.38 177 78 105 27 215.36 0.52 178 79 103 24 222.56 1.21 179 79 104 25 215.78 0.38 180 79 106 27 209.19 0.58 181 80 101 21 233.62 0.72 182 80 102 22 232.31 0.81 183 80 103 23 215.25 0.45 184 81 101 20 223.75 0.90 185 81 102 21 215.76 0.38 186 81 104 23 209.31 0.53 187 81 106 25 167.07 2.49 188 81 123 42 38.82 1.20 189 82 99 17 233.58 0.74 190 82 100 18 218.18 0.57 191 82 101 19 215.19 0.46 192 83 98 15 233.62 0.72 193 83 99 16 227.71 0.02 194 83 100 17 215.68 0.35 195 84 97 13 233.54 0.74 196 84 98 14 222.09 1.07 197 85 97 12 233.57 0.75 198 85 98 13 233.32 0.74 199 86 90 4 279.56 1.74 200 86 96 10 233.77 0.70 201 86 97 11 233.63 0.72 202 87 90 3 334.92 0.60 203 87 96 9 233.79 0.69 204 87 97 10 233.77 0.70 205 90 95 5 233.94 0.68 206 90 96 6 233.93 0.68 207 91 94 3 337.94 0.32 208 104 123 19 39.59 1.42 209 104 124 20 39.13 1.28 210 105 123 18 39.69 1.36 211 105 124 19 39.22 1.25 212 106 120 14 47.81 0.56 213 106 122 16 41.35 1.11 214 106 123 17 39.56 1.43 215 107 121 14 45.73 0.62 216 107 122 15 42.16 0.71 217 107 124 17 41.20 1.17 218 108 117 9 62.76 0.87 219 108 119 11 57.61 1.42 220 108 120 12 50.18 1.72 221 108 121 13 49.95 1.79 222 109 117 8 62.80 0.86 223 109 118 9 62.77 0.85 224 109 119 10 60.06 0.19 225 110 115 5 95.81 14.03 226 110 116 6 63.25 0.97 227 110 117 7 62.87 0.90 228 111 115 4 133.92 2.28 229 111 116 5 95.04 13.64 230 111 118 7 62.95 0.86 231 111 119 8 62.95 0.87 232 112 115 3 149.79 0.66